I am so confused. Looks like you could amplify your DNA using Klenow fragment to random priming. Then Why LM-PCR? Is it more sensitive?

-hn37041-

LM-PCR is more representative reportedly,

as for sensitivity, I think it's the same as random priming, although as the name suggests it is random, there could be some inherant biases towards particular regions of the genome and thus it becomes non-representative.

LM-PCR is more representative if you assume the primers ligate with equal efficency to all fragments within the genome.

Nick

-methylnick-

This makes sense. Thanks a lot!

-hn37041-

Hi, Methylink:

Could you please take a look at this protocol from AVIVA. I found people using different IP buffer. Not sure if this one would work. The elution buffer I used is 1xTE ,1%SDS

Thanks a lot!

-hn37041-

different salt and detergent conditions affect the binding of the antibody to it's antigen.

As for elution it is also the same thing so depending on your antibody/antigen you need to adjust the salt and detergent and invariably the pH of your buffer. It's a shame you don't know what "elution buffer" is made of, but your DNA should elute with your buffer.

you can test this with a IP-PCR on a known hypermethylated CpG island prior to arraying if that is what you intend to do.